Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Neural
Cell type
Neural Stem Cells
MeSH Description
Self-renewing cells that generate the main phenotypes of the nervous system in both the embryo and adult. Neural stem cells are precursors to both NEURONS and NEUROGLIA.

Attributes by original data submitter

Sample

source_name
NSC
cell line
NSC
cell type
Primary neural stem cells
genotype
Smchd1 GFP/GFP
strain
C57BL/6
chip antibody
Cell Signalling Technologies, D31H2

Sequenced DNA Library

library_name
GSM7134806
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
CTCF ChIP-seq libraries were prepared from approximately 15 million female NSCs using the ChIP-IT High Sensitivity kit (Active Motif), according to the manufacturer's instruction and 10 µg of CTCF antibody (Cell Signalling Technologies, D31H2). Libraries were generated with an Illumina TruSeq DNA Sample Preparation Kit. 200- to 400-bp fragments were size-selected with AMPure XP magnetic beads. Libraries were quantified with a D100 tape in a 4200 Tapestation (Agilent). Libraries were pooled and sequenced on the Illumina NextSeq2000 platform, with 75-bp single-end reads.

Sequencing Platform

instrument_model
NextSeq 2000

mm10

Number of total reads
55703933
Reads aligned (%)
96.6
Duplicates removed (%)
43.9
Number of peaks
16962 (qval < 1E-05)

mm9

Number of total reads
55703933
Reads aligned (%)
96.3
Duplicates removed (%)
43.9
Number of peaks
17032 (qval < 1E-05)

Base call quality data from DBCLS SRA